// ==========================================================================

// lambda

// ==========================================================================

// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>

// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin

// All rights reserved.

//

// This file is part of Lambda.

//

// Lambda is Free Software: you can redistribute it and/or modify it

// under the terms found in the LICENSE[.md|.rst] file distributed

// together with this file.

//

// Lambda is distributed in the hope that it will be useful,

// but WITHOUT ANY WARRANTY; without even the implied warranty of

// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

//

// ==========================================================================

// lambda.cpp: Main File for Lambda

// ==========================================================================

#include <sharg/all.hpp>

#include "mkindex.hpp"

#include "search.hpp"

#include "shared_options.hpp"

void parseCommandLineMain(int argc, char const ** argv);

int main(int argc, char const ** argv)

{

if (std::string(CMAKE_BUILD_TYPE) != "Release")

std::cerr << "WARNING: This binary is not built in release mode and will be much slower than it should be!\n";

int until = argc;

bool skipNext = false;

for (int i = 1; i < argc; ++i)

{

// version check expects a parameter

if (std::string(argv[i]) == "--version-check")

skipNext = true;

if (argv[i][0] != '-')

{

if (skipNext)

{

skipNext = false;

}

else

{

until = i + 1;

break;

}

}

}

try

{

parseCommandLineMain(until, argv);

}

catch (std::exception const & ext)

{

std::cerr << ext.what() << "\n";

return -1;

}

--until; // undo the "+ 1" above

std::string const subcommand_actual = argv[until];

if (subcommand_actual.starts_with("search"))

{

return searchMain(argc - until, argv + until);

}

else if (subcommand_actual.starts_with("mkindex"))

{

return mkindexMain(argc - until, argv + until);

}

else

{

// shouldn't be reached

std::cerr << "WRONG ARGUMENTS!\n";

return -1;

}

return 0;

}

void parseCommandLineMain(int argc, char const ** argv)

{

sharg::parser parser("lambda3", argc, argv, sharg::update_notifications::off);

parser.info.short_description = "Lambda, the Local Aligner for Massive Biological DatA.";

parser.info.synopsis.push_back("lambda3 [\\fIOPTIONS\\fP] COMMAND [\\fICOMMAND-OPTIONS\\fP]");

sharedSetup(parser);

std::string command{};

parser.add_positional_option(

command,

sharg::config{

.description = "The sub-program to execute. See above.",

.validator =

sharg::value_list_validator{"searchp", "searchn", "searchbs", "mkindexp", "mkindexn", "mkindexbs"}

});

parser.info.description.push_back("Available commands");

parser.info.description.push_back(

"\\fBsearchp \\fP– Perform a protein search (BLASTP, BLASTX, TBLASTN, TBLASTX).");

parser.info.description.push_back("\\fBsearchn \\fP– Perform a nucleotide search (BLASTN, MEGABLAST).");

parser.info.description.push_back("\\fBsearchbs \\fP– Perform a bisulfite search.");

parser.info.description.push_back("\\fBmkindexp \\fP– Create an index for protein searches.");

parser.info.description.push_back("\\fBmkindexn \\fP– Create an index for nucleotide searches.");

parser.info.description.push_back("\\fBmkindexbs\\fP– Create an index for bisulfite searches.");

parser.info.description.push_back(

"To view the help page for a specific command, simply run 'lambda command --help'.");

parser.parse();

}